autoencodix 0.2.1__tar.gz → 0.2.3__tar.gz

autoencodix-0.2.3/.gitignore

@@ -0,0 +1,10 @@
+data/
+notebooks/census_chunks/
+notebooks/*/*
+results/*
+Tutorials/DeepDives/acx_pretrained_models/*
+Tutorials/DeepDives/TutData/*
+*.pkl
+*.pth
+*.h5ad
+*.pyc

{autoencodix-0.2.1 → autoencodix-0.2.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: autoencodix
-Version: 0.2.1
+Version: 0.2.3
 Summary: Framework for multi-omics data integration by autoencoders.
 Project-URL: Homepage, https://github.com/jan-forest/autoencodix_package
 Project-URL: Issues, https://github.com/jan-forest/autoencodix_package/issues
@@ -30,6 +30,7 @@ Requires-Dist: pandas-stubs>=2.2.2.240807
 Requires-Dist: pandas>=2.2.3
 Requires-Dist: pyarrow>=19.0.1
 Requires-Dist: pydantic>=2.10.6
+Requires-Dist: python-dotenv>=1.2.1
 Requires-Dist: pyyaml>=6.0.2
 Requires-Dist: scanpy>=1.10.3
 Requires-Dist: scikit-learn>=1.6.1

{autoencodix-0.2.1 → autoencodix-0.2.3}/Tutorials/DeepDives/ConfigTutorial.ipynb

@@ -79,7 +79,7 @@
     "We can easily load the values into our config class with the `model_validate` method, as shown below:\n",
     "\n",
     "#### ❗❗ Requirements: Getting Tutorial Data ❗❗\n",
-    "To follow along, please download the date from the link below (1GB), if you've already done the `Ontix` Tutorial, you've probably already downloaded the data.\n",
+    "To follow along, please download the date from the link below (1GB), if you've already done the [`Ontix` Tutorial](../PipelineTutorials/Ontix.ipynb), you've probably already downloaded the data.\n",
     "\n",
     "https://cloud.scadsai.uni-leipzig.de/index.php/s/QXYnieKY8AA3Zta/download/OntixTutorialData.zip\n",
     "\n",
@@ -89,7 +89,7 @@
     "\n",
     "### Extra 2: Get correct path\n",
     "We assume you are in the root of the package. The following code ensures that the correct paths are used.\n",
-    "[1] Tutorials/DeepDives/ConfigTutorial.ipynb\n"
+    "[1] [Tutorials/DeepDives/ConfigTutorial.ipynb](./ConfigTutorial.ipynb)\n"
    ]
   },
   {

{autoencodix-0.2.1 → autoencodix-0.2.3}/Tutorials/DeepDives/EvaluateTutorial.ipynb

@@ -1653,7 +1653,7 @@
     "## Pure VAE comparison\n",
     "The function `xmodalix.evaluator.pure_vae_comparison()` is designed to evaluate the reconstruction capability of a XModalix (reference and translated) against a normal Imagix on the image target modality. This evaluation provides insights whether the enforced latent space alignment and coupled training in the XModalix decreases or improves the reconstruction capability in comparison to image-only autoencoder. \n",
     "\n",
-    "The prerequisite for this comparison is the prior training of an imagix. An example is provided in the XModalix tutorial. \n"
+    "The prerequisite for this comparison is the prior training of an imagix. An example is provided in the [XModalix tutorial](../PipelineTutorials/XModalix.ipynb). \n"
    ]
   },
   {

{autoencodix-0.2.1 → autoencodix-0.2.3}/Tutorials/DeepDives/ExplainStep.ipynb

@@ -30,7 +30,7 @@
     "\n",
     "#### Extra 2: Get correct path\n",
     "We assume you are in the root of the package. The following code ensures that the correct paths are used.\n",
-    "[1] Tutorials/DeepDives/ConfigTutorial.ipynb\n"
+    "[1] [Tutorials/DeepDives/ConfigTutorial.ipynb](./ConfigTutorial.ipynb)\n"
    ]
   },
   {
@@ -94,7 +94,7 @@
    "source": [
     "### 2a) Creating a synthetic ground truth\n",
     "Feature importance by attribution scores is hard to quantify for its performance and reliability of outcome. Hence, we will introduce in this tutorial a little synthetic signal on selected genes of a specific chromosome only for a group of sample to check if they will be picked up by our xAI method.\n",
-    "Hence, we will alter the gene expression and methylation intensities of some genes of the 21 Chromosome only for 'male' samples (compare also Ontix tutorial)."
+    "Hence, we will alter the gene expression and methylation intensities of some genes of the 21 Chromosome only for 'male' samples (compare also [Ontix tutorial](../PipelineTutorials/Ontix.ipynb))."
    ]
   },
   {